Figure 3

Distribution of Nrd1 and Nab3 motifs in protein coding regions. (A) Nrd1 and Nab3 preferentially bind near 5′ ends of mRNA transcripts. Shown are pyBinCollector coverage plots displaying the Nrd1 and Nab3 motif distribution in the exons and UTRs of all non-intronic mRNAs. To normalize the gene lengths the exon sequences were divided in 130 bins and UTRs in 10 bins. Probabilities were calculated by dividing the density values for cross-linked motifs found in the PAR-CLIP data by the density values for all the motifs found in mRNA coding genes. (B) Heat map showing the distribution of cross-linked Nrd1 and Nab3 motifs (blue) over individual protein coding genes. pyBinCollector was used to produce a distribution matrix of cross-linked motifs over individual protein coding sequences and the resulting output was k-means clustered using Cluster 3.0. (C) Distribution of cross-linked Nrd1 and Nab3 motifs around stop codons and relative to the positions of polyadenylation sites.